Mass Effect: Factor X
by Worldwalker14
Summary: Shepard is dead. All hope seems lost. Yet when Ceberus rises and concentrates on an ambitious project, like a newly lit candle, hope flickers. However, despair settles in when complications stand in the way; notwithstanding, a mysterious figure comes and helps the project progress. Who is this individual? And what's the purpose? Here, the story unfolds.
1. Chapter 1

**Note: Hello, my friends, I have another important announcement to make: In the past, while reading this very fanfic, I was drawn to it and became its instant follower. The writing was good, the storyline was special and intriguing. It's a shame the owner, Knight on Bald Mountain, decided to abandon it. Now, seeing as I'm a huge Samus admirer, and a fan of the Mass Effect series ( no 3, please ), I have asked Knight on Bald Mountain for permission to continue it. And he agreed. I know my style is different from his and may be inferior to his, but I will do my damnedest to stay pretty true to the original. I don't own either Metroid or Mass Effect franchise, all credits belong to the original creators. Please review after you read. Thank you.**

 **Prologue**

The SSV Normandy was gone. Nothing more than a memory. Within just a couple of minutes, the majestic work of engineering now became an empty husk of metal. Its broad and shining armor now burnt and torn, anything that resembled a ship had now vanished. It would have been a spectacle to behold, had it not been for the deaths of the many crew members, and the loss of one particular soldier.

His name was Shepard. Commander John Shepard. A defender of the Alliance from a threat that it wasn't even believed to exist; his determination, skills and cunningness brought an end to the horrific Reaper known only as Sovereign. Though the threat of the Reapers had been postponed, it was by no means, over, as this expedient encounter with the Normandy clearly proved. Of course, none of the Council would admit it was them. In their willful ignorance, they'd wipe the memory of the Reapers away and replace it with something less apocalyptic to keep the people from panicking, to keep them their obedient sheep.

Suffice to say, any hope of saving the known galaxy seemed lost, for the one man who could stop it all, was dead and lost.

Two years have passed since his death. What would happen next, no one in the Alliance could have anticipated.

Well, Cerberus happened. Held up as a radical human rights terrorist cell, they poured in billions of credits into the recovery and resurrection program for the Commander, codenamed The Lazarus Project, using cybernetic implants, skin reconstruction and special fluids to bring the dead man back to life. It looked to be a lost cause, however; it seemed as if it all just wasn't enough. They had all the resources, but they needed something extra to make it all work.

Word was secretly leaked that a "top secret" organization needed donors to supply ample amounts of blood for the use of DNA splicing. Many volunteered. Some were accepted, most were turned away. None of them worked. For a while, it seemed as though the project would stagnate and expire; but the Illusive Man, the head of Cerberus, would rather spend another fortune than to see it all disappear.

That was when it happened. A mysterious subject, out of nowhere, donated two pints of her blood. She charged an incredible amount of money for it, but it turned out to be exactly what was needed. She had the X factor. The scientists on the project had no idea what it was, and almost feared injecting it into the Commander, but they had no other options. The moment they did it, the process began to work. Slowly and steadily, the corpse began to regenerate. Everything quickly began to fall into place.

Commander Shepherd's return was estimated to be complete in a couple of weeks. The female stranger was contacted again; a request for another two pints of blood was made to finalize the project. She refused. Several attempts were made to sway her, but all were declined. It was not enough to stop the Illusive Man. He sent an operative to speak to her in person. He would get her into contact with him, and they would discuss it in private.

Though skeptical about the whole ordeal, she accepted. She was escorted to the Lazarus Research Station and led to the conference room. There, they left her alone and shut the door. That was when the hologram came up, and there he was: the Illusive Man. Sitting comfortably in his chair while nonchalantly smoking his cigar. For a good minute, he didn't even say a word. He just observed the woman before him.

She wore a giant suit of armor, covering her entire body, adding almost a foot in height, he estimated. Had it not been for the green visor on her helmet, he might not have been able to even tell it was a woman at all. The way she stood lacked a basic femininity that he saw in Miranda Lawson, nonetheless, one of his chief officers. There was a presence that she exuded, just standing there waiting on him. He had many questions for her, and this was perhaps the only chance he'd have to ask them.

"I'm glad you accepted my offer to see me", he began, finishing another puff a smoke, "let me first thank you for your incredibly generous donation to our project. It never would have been properly started without your help".

"Thank you for you generous offer of credits". Her voice was soft but firm. The deeper tones suggested elegance as well. "But now I'm afraid that I can't offer anymore".

"Certainly, you didn't come all the way here to just tell me that you weren't going to donate your blood".

"Perhaps I'm trusting that telling you directly will stop your attempts to take it by force".

"I instructed my people to convince you to give it to us willingly. If they attempted to kill you in the process, that was an error on their part. Not mine".

"I've been studying your group for some time. You're very good at absolving yourself of any responsibility. I prefer working for people who are trustworthy".

"Then why did you come to us in the first place?".

The woman halted briefly before answering:"Because I needed money".

"That can't be all". The Illusive Man grinned mildly, catching her in a half-truth. "Or else, you wouldn't care about our trust then".

The woman remained silent, giving the Illusive Man another moment to try to read her. She had strong body control; even under his mild interrogation, she made no apparent movements to indicate hesitation. Whatever it was she wanted, she did very well to hide it. Of course, the armor didn't help. "Would you mind removing you helmet? I would like to see who I'm negotiating with".

"Not a chance". A quick rejection with no follow up. The Illusive Man decided to move on.

"You know, you are a hard woman to track. I've had several of my operatives track your past. Would you like to hear what they found after three months of investigation?". The woman didn't respond verbally nor physically. "Nothing other than that you suddenly appeared in the colonies near the Veil about a year ago".

There was a slight hint of movement inside the armor, perhaps a chuckle. It was hard to tell. Still, he was not finished. "Now I pride myself in knowing everything about everyone I believe to be important, and when I can't do that, I am left to believe that there is something extraordinary about that person. It doesn't help that when you donated your blood the first time, even my scientists don't know what to make of it".

"Perhaps I'm a by-product of a biological project", she chided him. The Illusive Man did not appreciate being talked down like a child.

"Don't abuse your privilege to speak with me with your taunts. My scientists believe that your genetic code has been tampered with, for the better. We at Cerberus believe in anything that will serve the betterment of Mankind, and that code could hold a vital key to make us the dominant species in the galaxy".

"Which is why you want two more pints of blood", the mysterious woman surmised.

"I've never hid my intentions. We do need two more pints of your blood to finish the regeneration of Commander Shepard. I'm also asking that when you're ready to donate another two pints for genetic research, that you would do so. We are willing to double your payment for the second donation, and triple the third".

Again there was silence from the armored woman. She clearly had to think this one through. Perhaps the Illusive Man was starting to get through to her.

"I'm sorry, but I'm not going to donate my blood for your own research".

"Then, will you at least do it for the Commander? At least finish what you started".

"On one condition". She took a step closer towards the holographic projection of the seated gentleman. "I stay here to make sure that it's used properly. If for even a second it's used outside the Lazarus Project, or if there is anymore attempts on my life, I'll make sure you never see the results".

"Agreed". He didn't even bother to consider anything else. The life of Commander Shepard was of paramount importance, and everything else came second. "Send in Ms. Lawson and I'll have her make arrangements for your stay".

A mere second later, the door behind her opened, and a tall, well-figured woman strutted into the room, not even waiting for the other woman to leave. "You wanted to see me?".

"Miranda, please ensure that our donor has a place to stay here until Commander Shepard is completely revived. She is our guest and will be treated as such".

"Of course, Illusive Man".

"Miranda". It was a command, not a question.

"Yes?".

"Do not eavesdrop on my private conversations with guests. One more time and there'll be severe consequences".

"Of course, Illusive Man", she repeated herself, like a trained parrot.

Next, she turned to face the armored woman, gesturing for her to follow. "This way, Ms. Aran".

The armored woman nodded as she began up the steps. "Just call me Samus".


	2. Chapter 2

**Note: I don't own either Metroid or Mass Effect franchise, all credits belong to the original creators. Please review after you read. Thank you.**

 **Chapter I - The Lazarus Crisis**

At first, he felt nothing. Then came a mild rumbling, almost too subtle to feel. It started to get stronger, but it wasn't enough to wake him. That was when his ears began to pick it up, a voice was shouting at him, commanding him to wake up. He wasn't sure if it was all a dream or if it was reality. It took a moment for him to finally realize something wasn't right.

He was alive.

He would have begun to ponder why that was, had somebody- No, a woman! Had a woman not shouted at him.

"Commander Shepard! You have to wake up, now!", she urged.

And then, he began to opened his eyes. Standing over him was someone in heavy battle armor. Through the green visor on the helmet, he saw the woman's eyes; they bore a look of deep concern. Ashley Williams had given him that look just before he went to grab Joker the day the Normandy was attacked. How long ago was that? He thought to himself. It felt like it was a distant memory, but he remembered it so clearly.

"Commander Shepard!". The woman's voice was now loud enough to leave a ringing in his ears. "The station is falling apart! I need you to get up. We don't have time to waste!".

Shepard wasn't one to take orders from unknown people, but as far as he could tell, she was right. The rumblings he had heard from before were caused by explosions, and they were getting louder by the passing moment. If they were to escape, they'd need to move quickly. Finally, Shepard stood up. Now he felt a throbbing pain in his head. He was almost certain it was going to explode.

"Over there! Quick, there's some armor and a pistol set down just for you". The woman pointed towards the cache of armor. And her right arm made him notice that there was a giant cannon fixed on it. However, he didn't have time to admire it, study it and even try to persuade the woman to let him take it apart and examine it, since he needed to suit up before anything happened.

He took that moment to ask a quick question:"What's the situation?".

"Somebody has set charges at a number of critical areas on this station", the woman stated, now in a calmer tone, "then that somebody set off the LOKI and YMIR security mechs friend-foe identifier to keep everyone else occupied while they escaped".

"Is this a research station?", the Commander asked, just as he was almost done with suiting up.

The woman nodded, which lead to his next question. "If someone wanted us all dead, why not just set off the self-destruct?".

"I don't know, but I assume it's because it wasn't Miranda who's trying to kill us. I believe she's the only one who could override such an order. Besides, I think this person wants you dead more than anything. You weren't supposed to be ready for another three days. My thought is they was hoping they'd come here first. You're lucky I saw them first, or they may have succeeded".

Shepard nodded, but did not reply. He still had some suspicions about his current situation. Perhaps the woman was just staging him for a death elsewhere. It didn't help improve that impression at all, when he picked up his pistol, his empty pistol. "This pistol doesn't have a thermal clip".

"I'm sure you'll find plenty on the dead LOKIs and YMIRs. Until then, I'll be taking care of them", the mysterious female replied.

Next, she started heading for the door. Then, she halted and turned back to Shepard.

"The shuttle bay is a little ways off. Are you ready?", she inquired him.

"Just one question: What happened to me?".

"Long story short: you died. Two years later, we brought you back. Welcome back". The woman already began heading towards the door when she stopped. She turned to him once more. "By the way, my name is Samus. Samus Aran".

...

Shepard had originally intended to ask more questions while they ran, but he was still a bit disoriented, and lacked the focus to do so at the moment. The two quickly rushed through the next door, Samus checking all corners of the room before signaling to him that the coast was clear. They turned up a ramp to follow a trail that Samus clearly knew very well. There was no question that she knew exactly where she was going. For a short while, they had virtually no complications. That was when the mechs began to appear. There were six of them, all gunning down at them with a monotone "HOSTILES DETECTED".

"Get down!", Samus shouted as she quickly engaged their adversaries.

Shepard did as he was told, and watched in awe as the fearless woman simply ran towards them with her arm cannon firing rapid shots of what appeared to be electrical currents. Each one went down after about two shots. The rounds that were fired after her deflected harmlessly off her armor. Within a matter of seconds, the mechs were just heaps of smoldering metal and badly damaged electronics on the ground.

 _Damn, that was some reflexes._

Shepard quickly got back up and grabbed the thermal clips left behind. He couldn't help but wonder what Samus' story could be. But while the explosions were still going off, he didn't wish to pry until they were safely away on a shuttle to anywhere but here. Just a couple of seconds later, they found another survivor taking cover behind a guardrail, firing his pistol at another set of mechs. He was a dark-skinned human. The mechs hadn't yet spotted the two newcomers, so Shepard took the opportunity to fire his pistol at the mechs. Being dead definitely made him a bit rusty, yet he still was quite capable at cutting them all down with speed and intensity. The younger man quickly spun his head around to look at his rescuers.

"Shepard? Aren't you still supposed to be under wraps?". He was surprised.

"That's what I was told, but if this place is coming down, I don't think it really matters as long as we all get out of here alive", the Commander answered firmly.

"I suppose that's true. I also suppose that your friend here was the one who woke you". The younger man motioned to Samus.

"I did what I had to", Samus calmly said, "I doubt Miranda would like it if we all, but him, escaped".

"Of course, Samus", the second man deadpanned, "I'm just surprised you were able to do it. You look more like a battering ram than a biomedical specialist".

"I have a LOT of surprises, Jacob", Samus emphasized.

"I know we all have lots of questions". Shepard interfered. "But if this place is coming down like I've been told, we'd best get out now. We can talk along the way".

"You're right, Shepherd". Jacob nodded. "You're going right to get to the shuttle bay. I guess I'll be tagging along then".

After that, the trio expeditiously moved on. Moments later, the first question came from Jacob. "Have either of you even seen or heard about Miranda yet?".

"Not a word", Samus responded simply.

Shepard, beginning to recover from his headache, replied with another question:"Is Miranda in charge of this station?".

"Technically", Jacob answered, "she was the one overseeing your regeneration. She along with Wilson, but he answered to her".

"And who do you all work for?".

Jacob had to halt first, debating whether or not he should answered truthfully. Samus, on the other hand didn't care, speaking quickly:"I'm a freelancer, but your friends here on the station are part of Cerberus".

Shepard stopped completely. He had to think about this.

"I remember Cerberus pretty well. They had some horrific experiments going on that I had to stop", he commented.

"I won't lie to you", Jacob interjected, knowing that deceiving him now would not bring him any good, "I myself don't trust everything that's been done, but they brought you back for a good reason. I only joined recently because the Alliance is not doing a good enough job protecting the galaxy".

"You're referring to the Reapers?". Jacob nodded. "All right, I'll follow for now, but I don't plan to help any of Cerberus' terrorist activities".

"That's all I'm asking right now".

"And don't forget that", Samus emphasized again, "because I'm with Shepard on this".

 _She is?_

After a couple more rooms, Shepard and the others ran into another group of mechs, hovering over a limping scientist. The three tried to catch him in time, but they were too far to reach.

"TARGET ACQUIRED".

"No, stop!". The scientist pulled the trigger on his pistol, but it didn't fire. He was out of ammo. He cursed silently as the mechs fired at him one last time:"Why do these things never work at proper mo-".

"Damn it!", Jacob swore, causing the mechs to turn to face their new acquisition.

The three humans quickly laid down a barrage of fire at the mechs, dropping them down before they even had a chance to fire back. Jacob was headed over to see who they just lost.

"It's Wilson", he reported to Shepard and Samus, "didn't even stand a chance. If we'd been here just a little bit sooner...".

"I don't know", Samus pondered, "he left a very brief blood trail, and it's leading from the mech control terminal".

"Maybe he was trying to shut them down", Jacob suggested.

"Maybe", Samus debilitated the possibility, "we should get going".

The others nodded and continued along the path towards the shuttles. Finally, they reached the cargo bay. The vast open area was littered with all sorts of boxes and crates. The shuttles would be up the walkway; nevertheless, as bad luck would have it, one of the explosions had blocked the path to the shuttles. To make matters worse, they were suddenly being flanked by a score of mechs.

Samus turned around to face the ones behind them, firing another set of electrical waves at her targets, while Shepard and Jacob took cover, slowly whittling away at the ones in front. The two soldiers worked well together, with Jacob using his biotic powers to pull the mechs helplessly forward, and Shepard setting them off with a pair of rounds to the heads. The mechs were too stupid to use cover properly, having only limited programing, making it easier for the trio to eliminate their targets swiftly. The only problem, was that they were more persistent than most organic threats, and they usually had a nonstop barrage of fire going over them. Though the two men took some minor hits, they were able to dispatch the last of their opponents with relative quickness and ease.

With the active threat out of the way, they now only needed to get rid of the debris in front of the shuttle bay door. Samus decided she was the one to solve this problem.

"Get behind me", she told her male companions.

The two men acknowledged as she began to charge her arm cannon. Once it reached a decent size, she fired off a missile. The blast annihilated the debris and even the door, while still leaving the infrastructure intact. _Impressive weaponry._ Thought both men in wonder. As the smoke cleared, they were surprised to see that someone was on the other side. It was Miranda Lawson.

"Well, well, well", she began, "I was wondering when you'd show up".

"If you were worried about time, you should have come and help us, Miranda", Jacob accused her.

"In case you didn't notice, the door was blocked."

"So you just happened to be waiting in the shuttle bay before this attack started?", Samus questioned the other female.

"I knew the mechs were a distraction, and came here to make sure that there was an escape for us all", Miranda replied.

"Alright, ladies, enough", Shepard intervened, "we can argue on board the shuttle".

"Shepard's right... again". Jacob couldn't help but smile, knowing that the former corpse was already establishing his authority.

"Very well, then. Let's get going". Miranda turned towards the armored woman. "And since you're up early, I'll need to ask you some questions along the way to see how you're holding up. I assume your work here is done?".

"Unlikely. I'll be following you closely. Wherever Shepard goes, I go", Samus replied as she began to separate herself from the others, heading towards her own ship, docked next to the shuttle. And her answer surprised Shepard.

 _Why is she taking my side? What is her agenda here? Or is she just... interested in me?_

Then again, there was her ship. Shepard couldn't help but noticed how particularly odd it looked. It had a yellowish color and was as big as a fighter. Everything about that woman kept giving him more questions. She intrigued him.

The shuttle ride was long and full of all sorts of questions: Miranda asking about Shepard, recalling all his previous decisions from saving the Council to leaving Lieutenant Alenko behind on Virmire. She picked his brain quite a lot too. Then, it was his turn, asking about the Lazarus Project, what Cerberus wanted with him, but mostly about Samus. Miranda was quite happy to explain the details of the Lazarus Project, but also explained that the Illusive Man, the head of the Cerberus, would certainly explain what he wanted from him. As to who Samus really was, they really didn't know. All Miranda could say was that she was given an incredible amount of credits to help donate to the project, but she didn't trust Cerberus. And it became quite obvious to Shepard that Miranda didn't like her at all.

They soon boarded a small gateway station in a nearby system. Miranda said that she'd put Shepard in contact with her boss, the Illusive Man, so that he knew what exactly was happening and what was expected of him. The last part did not sit well with the Commander, but Samus told him that he was still his own boss, and that he should just ignore the latter part of Miranda's statement. Miranda made quick work setting up the conference hologram. Within mere minutes, the three survivors of the Lazarus Project were seated in the waiting room while Shepard marched into the Illusive Man's holochamber.

The room lit up as a grid-like analysis dictated where precisely to put the Illusive Man. Another couple of seconds and it slowly generated the moving image of the Illusive Man. Still sitting on his favorite chair, smoking another cigar.

"Shepard". His voice was almost casual, but still held an air of confidence. "It's good to see that you're back among the living".

"Illusive Man", Shepard responded with equal confidence. His words simply floated in the air briefly, as if to see his reaction to hearing his name, or rather, what he was called, "I don't know why you brought me back, but I'm telling you now that I don't work with terrorists".

The Illusive Man took another puff of his cigar. "Shepard, you, more than anyone, know that the threat we face is much greater than you and me. I ordered your recovery because not only are you a charismatic leader, but also the only one who truly understands that threat".

"You're telling me your only thoughts were to protect the galaxy from the Reapers?". Shepard sneered.

"Shepard", The Illusive Man responded patiently, "your actions two years ago on the Citadel proved that humanity was ready to step up. You risked human lives to save the Destiny Ascension and the Council, something I wouldn't have done, but you gained their trust".

"Now... ". The Illusive Man halted as he took another puff. "They ignore the loss of our colonies and pretend that the Reapers are still no more than a geth myth. Regardless of what you think of us here at Cerberus, we're the only ones that can help you".

Shepard gave him an inquisitive look. "You said something about the 'loss of our colonies' ".

"Entire colonies are being abducted by unknown assailants. One hour before, they were running perfectly, another, we completely lost contact with them; and then, every member on that colony was gone without a trace. My sources believed that it was the work of the Reapers, but they're using someone else to do their dirt work".

"We have one lead right now". Out came another puff of smoke. "The colony Freedom's Progress. Our last communication with them was four hours ago. I suggest that you go there quickly before someone else investigates".

"Is that a suggestion, or an order?". Shepard hardened his voice.

"As I've said before, I'm offering to help you. I can only supply you with information and assistance. If you wish to reject it, that's your prerogative, but you should really go to Freedom's Progress first, and see it with your own eyes. I'll have Miranda and Jacob take you there on one of our shuttles".

"I'm not so sure I can trust them. They work for you, not for me".

The Illusive Man smirked. "Miranda is loyal to me, yes, but she'll follow you as long as I tell her to. Jacob is more akin to you than you think. If you can trust anyone here, it's him".

"And what of the other woman, Samus?".

The Illusive Man sat silently for a second. He seemed to find that name a bit distasteful. "Her relation with us ended when you woke up. If you want her help, the choice is yours". His voice was coolly calm.

The Commander stood there in thought for a while. He wasn't sure what to think of it all. The Illusive Man was quite accusatory of the Council and their attempts to cover up the Reapers, though Shepard was aware that they were still remise of the idea. He found it difficult to believe that they'd ignore such a threat of this magnitude. Perhaps the Illusive Man was right, at the very least, he could trust him to help him.

"Okay, I'll get over there as soon as possible, but keep in mind that I'm in charge of this operation".

"That's good, Shepard. Miranda will have you flown over to Freedom's Progress whenever you're ready". The Illusive Man smiled satisfactorily.

The hologram slowly began to fade. Shepard took time to leave the room. He even continued to walk past Miranda back to the shuttle while he informed her of their new task.

"We're leaving for Freedom's Progress. I'm trusting your boss for now".

"If anything, we're taking a risk for trusting you", Miranda countered as she fell into step behind him, "I know you don't have Cerberus' interests at heart".

"The galaxy is bigger than just us humans". Samus pointed out, starting ahead of them both. "I'll be following you again on my ship".

"Samus". Shepard stopped her. "I don't know you, and though we both don't care for Cerberus, I'm not sure I want you along".

Samus was shocked at his response. "I saved your life, and not for any motive other than the fact that we need you".

"Now I'm going to follow you whether you like it or not". She insisted.

The armored woman stormed off towards her ship, giving Jacob ample time to catch up to the other two standing there. "I don't know about her, but I still got a feeling she's hiding something".

"And the Illusive Man isn't?", Shepard countered. He, then, called out for Samus' attention. "Will you follow my orders?".

"To the letter".

 _To the letter. Well, we'll see._

"Then you can come along".

Under her helmet, a smile streaked across Samus' face.


	3. Chapter 3

**Note: Because I fucked up the classification of the Prologue, naming it Chapter I, instead of... well, the Prologue, so Chapter II will become Chapter III, and I can't do anything to UNdo it. Talk about irritating mistakes. Anyway, please read and review, thank you.**

 **Chapter II - Halted Progress**

Shepard rested his head against the chair. His headache was still causing a problem, and it didn't help that their landing on Freedom's Progress was taking longer than desired. Jacob seemed to have some difficulties compensating for the lack of space: All docking bays were still occupied, and the closest clear landing was three kilometers away; and though not an unbearable distance at all, it was time that would be wasted. Therefore, landing upon open areas inside the colony itself, was the only option available. While Samus' ship seemed at ease at hovering on top of a building, Jacob was attempting a slow descent down on what appeared to be a merchant district covered with crates.

Eventually, they were able to land. Shepard grabbed an assault rifle and sniper rifle off a weapons rack, checking the scopes and barrels of both, and when he was satisfied, he holstered them on his armor. He looked at both Jacob and Miranda, who were ready as well. He motioned with his hand to move out. When they were outside, they could see Samus Aran on top of the building where she had landed. She hopped down with hardly a care and approached them. Shepard followed suit and closed the gap.

The armored woman spoke first:"Every building and structure here seems to be in perfect condition. It's like there was no conflict at all".

"But everybody's still gone". Jacob pointed out. "So whoever is attacking colonies has been here and away".

"Which means, they're able to clean them all without even a struggle", Miranda proposed, "if we're lucky, some must have hid to avoid detection".

"Searching for survivors sounds like the best idea". Shepard nodded. "We'll do that. I want us to stay close together, and keep your eyes open for any movement".

At Shepard's orders, they all began to follow the Commander around the colony. They were cautious, moving at a leisurely pace just to be sure they didn't overlook anything. After two minutes of trudging around empty buildings, they found something they did not expect: Several LOKI mechs began to activate at their presence and began to attack. The four combatants quickly dispatched a couple of them, but were quickly flanked by a couple of FENRIS mechs. They charged directly at Samus, leaping at her with one quick motion. Their taser devices shocked her armor, causing her to grunt, but it seemed to only slow her for a second while she turned to face her new targets. She fired her arm cannon at them as quickly and precisely as she could. When she returned to the others, they had already finished the LOKIs.

Jacob was the first to speak. "The security systems shouldn't be active. Someone has to be here".

Miranda pondered out loud:"We don't know for sure. They might have been activated during the assault".

"They would have fought back when they were attacked", Samus interjected.

"Since we don't know how the people were abducted, it's possible they never encountered anything", Miranda countered.

 _Uhhh, not again._

"That probably would indicate that they were being abducted from space, which would also indicate that activating the mechs would have changed nothing". Samus stood her ground.

"I'm not trying to dictate how everything happened". Miranda took a step towards Samus. "I'm only rationalizing any possible outcome in a situation that we have little intel on".

"If you two are going to just argue the whole time, then I want you both to get back to the shuttle. If not, then shut up and move on, alright?". The Commander's voice was cold, yet it couldn't contain the tone of irritation.

Shepard didn't even bother looking back at them as he continued to walk forwards to survey the area. Samus and Miranda looked at him, and then back at each other. Samus was the first to go after him while Miranda took a moment before she did so. Shepard glanced back just to make sure that Samus was keeping her "to the letter" promise. _So far so good. But I'm not gonna trust you 100%... yet._ However, of the three people accompanying him, he trusted Miranda the least. He could tell. Because of the way she spoke of the Illusive Man as they were on their way to the gateway station. The only thing he felt that she was honest about was her loyalty to that man. He did notice a couple other things, nonetheless: First, she had proven to be capable with a pistol in that last fight. Second, she also showed off a number of biotic abilities that put most adepts to shame. And finally, the way she looked, with her long, dark hair and powerful eyes; it was as if everything about her was trying to produce a sense of perfection.

Jacob, on the other hand, was different. He seemed to admire Shepard, ready to listen and do whatever he said. He felt he could trust him. _Like me trusting a pet? Hmm..._ Plus, after listening to the story about the time when he was in the Alliance, Shepard felt more at ease with him. Having Alliance training also showed his effectiveness in combat which seemed to overbear Miranda's. It helped make up for his weaker biotic abilities, to be sure. His eyes didn't seem to show any presence at all. They were just always searching, as if they were looking for something and he still couldn't find it. Then, there was Samus. The mysterious woman had just taken a spot next to Shepard. He still couldn't get a bead on what her intentions were. Since they were heading towards the cargo docks, he figured it'd be best to try and get to know her better.

He started with something simple. "I've seen a full grown man go into shock when attacked by a group of FENRIS mechs that big... even in armor. How well does that thing protect you?".

Samus pondered briefly whether or not to answer, but she seemed to not mind this time. "It's the best there is. Of course, they're not made anymore, and are really hard to get your hands on", she said, her voice sounding a bit... _boastful?_

Shepard was totally impressed. "Nice. It certainly is a tough chunk of armor, no doubt about it. Did all those armaments come with it?". He was eager to know more.

"Not all, really. I mean, I had to find upgrades here and there for many years". She took a moment to point out a number of her weapons. "My arm cannon uses several different beam weapons along with a couple of missile components. You've seen me using my wave beam, which fires electrical bolts and occasionally will fire through walls when I charge it, but I also have an ice beam and plasma beam. Normally, though, I just use the power beam". _Now she sounds amusedly proud, she's almost cute. Wait a minute, "cute"?_

Samus was about to go on, but she stopped suddenly. _Uh, why did you stop?_ Shepard was disappointed. His mysterious female companion pointed towards one of the buildings.

"My thermal scanner is picking up a number of humanoids in that structure".

"Perhaps they are survivors", Shepard suggested. "We'll start over there, but stay on your guard".

Shepard signaled for his team to follow him over to the destination of their new objective. They quietly approached the building, setting themselves up for a breaching sequence, with Miranda and Jacob at the sides of the door, Samus as the point gunner, while Shepherd opening the door. On his count to three, he had the door opened and all his operatives aimed inside. To everyone's surprise, they were greeted by more weapons, weapons from Quarians.

"Cerberus operatives!", One of them, a male, shouted, "give us one reason not to shoot you now!".

"Dammit, Prazza!", Another one, female, swore as she walked at the lead and swatted the male's hand from his current target, "This is my mission, you listen to me".

She, then, turned to face the intruders, and what she saw astonished her. "Shepard? Is it really you?".

Shepherd quickly realized that the female Quarian was none other than Tali'zorah vas Neema, a young engineer who had joined him on his hunt for Saren. She was even wearing the same protective environmental suit that she'd had the first day they met. He remembered it very clearly: The young female trying to make a deal with the Shadow Broker only to be ambushed by one of Saren's men. She'd dealt with him rather quickly, putting her combat training to the test. The young female knew how to take care of herself, yet still chose to follow Shepard to the furthest corners of the galaxy. He found it extremely surprising to see her.

"Tali? What brings you to Freedom's Progress?".

"I think a better question is how are you still alive... and with Cerberus?". She had taken a step back, still cautious.

She was familiar with practically all things mechanical and artificial, and she wouldn't put it past a demented group like Cerberus to have created some sort of clone or something else of the greatest human warrior she'd ever known.

Shepard smiled simply at her before responding:"Cerberus put me back together. In return, I'm checking out the disappearance of human colonies".

"Don't trust him, Tali", The Quarian Tali had just called Prazza, interrupted.

She turned towards him, her momentary distrust of the Commander instantly vanished when he questioned her decision-making.

"Commander Shepard was the one who gave me the data on the geth in the Armstrong Nebula. I have every reason to believe him".

Tali turned back to her old friend. Shepard had not considered the possibility that she would command a unit. Then again, her father was the leader of the Admiralty Board of the Quarian Migrant Fleet. Leadership probably came naturally to her.

"I'd like to help you, but we are looking for someone here on your colony. Another Quarian named Veetor".

"Do Quarians normally find their way to human colonies?", Jacob asked, honestly unaware of their culture.

"Veetor was on his Pilgrimage. He felt secure helping more secluded locations where there are fewer people around. The point is that he's still here, and we need to find him".

"Do you think he's the one that activated the mechs?". Samus was next to inquire Tali.

"Unfortunately. He is a bit unstable as well, and he suffered some damage to his suit. We believe that the subsequent infection has made him even more so", Tali stated matter-of-factly.

"If he was here when the abductions happened, we'll need to talk to him", Miranda deduced.

Nevertheless, Tali was not yet ready to seal any deal. "Shepard, I would appreciate your help, but if you are with Cerberus, I have to know now whether or not you're going to prevent us from taking him back to the flotilla".

"You know I'm not going to stop you. What could Cerberus have done to make you think that?".

"An attack on our fleet and the death of our people", Prazza interrupted again.

This time, Tali nodded in confirmation.

"That's not exactly what happened". Miranda felt the need to defend her boss, once again showing her fierce loyalty to him.

Samus rolled her eyes. "With the way the Illusive Man runs things, I wouldn't be surprised if it's exactly what happened".

Miranda gave her a cold stare, but Samus' armor must have reflected it because she didn't care.

Shepard quickly cooled the situation before it got out of hand, again. "The sooner we help you, the sooner we can find out what happened. What's your plan, Tali?".

Tali shrugged. "He was last seen at the cargo docks. We aren't as well-equipped to deal with all the mechs. If you can head out first and draw their attention, we'll sneak around and try to get to him".

"And have us do all the dirty work? Typical Quarian plan". Miranda rolled her eyes.

Prazza only became angrier. "Your friend's companions are only giving me more reason to not trust him. Why do you insist on having us do so?".

Tali grunted in annoyance. "Because I trust the Commander more than I trust you".

That shut him up. Though Shepherd couldn't see past his suit's visor, he could tell he was furious by her remark.

He turned to face Tali once more before preparing to head out. "We'll do it. Keep in radio contact, should anything come up".

"On it, Shepard".

Tali took that moment to talk to her troops in private as the humans left. Next, Samus took the point this time while Shepard took a step back to guard the rear. The team was no more than a hundred yards away from Tali before they heard her over their comms.

"Watch out, Shepard. I'm detecting a number of assault drones heading your way!".

As if on cue, a number of drones flew overhead and began to set themselves up along the tops of several buildings and structures. Then, they began to bare their weapons on them, but the four humans were able to find cover before they opened fire.

Shepherd replied in mild sarcasm. "Thanks for the heads up, Tali".

Samus took a quick glance over her cover to check the drones' positions. They immediately opened fire on her. Her reflexes allowed her to drop back down before taking any damage to her armor.

"Enjoying the view?", Miranda asked, not even attempting to mask her taunt.

Samus just ignored her and spoke to Shepard. "Three of them are standard assault drones, while two are of the rocket variant. If you can draw their fire for just a couple seconds, I can get behind them before they can react".

 _Ah, the screw attack. Awesome._

Shepard nodded. "Shields won't last long with the rocket drones. I'd estimate about five seconds before we drop back down".

"That's all I need".

Without another word, Samus' armor morphed into a perfect sphere, about a meter in diameter. Shepard was stunned. _What in the black hole?_

And Shepard would have kept on gazing at that 'sphere of wonder', if not for Jacob to elbow him slightly. Shaking his head lightly, he signaled for his companions to open fire on the drones. They held their own for a couple of seconds, soon finding their shields nearly overwhelmed, dropping back down. They had only downed one assault drone and heavily damaged one of the rocket drones. After waiting for approximately a minute, they heard the sound of Samus' wave beam. After that, every drone was destroyed.

Shepard heard Tali's voice over his comm. "All clear".

Shepherd was the first to get back up. Unlike his companions, he was able to hide another take of his amazement when he found himself staring at Samus as she approached from atop the buildings.

However, Jacob was quickest to ask:"How the hell did you do that?".

Samus dropped to their level and continued to take the point along the given path. "Came with the suit. Of course, it takes years of practice to perfect it".

 _She finds "upgrades here and there for many years", then "it takes years of practice" for her to perfect her combat performances. Now ain't that intense? I think I'm beginning to like her already._

Shepard found himself smiling as the rest of them got back into formation. He couldn't help himself even as a small chuckle escaped his mouth. The others noticed, but felt no need to acknowledge it. Following that, they proceeded to follow Samus' lead. Soon, they reached a great door sectioning off their area. That was when they heard Tali over their comms again.

"Shepard! Prazza and his men have moved ahead. I told them to stop, but they wouldn't listen. They still don't trust you to give us Veetor when you're done!".

"Of course", Miranda declared, rolling her eyes again, "and we didn't even make a move against them. Just like the flottila incident".

"I'm really starting to dislike you, Miranda", Samus stated coldly.

"Really? I started the moment the Illusive Man told me to make room for you onboard my station".

"Is this really the time for that?". Jacob was getting tired of the two women bickering.

 _I know, Jacob. I asked that question myself twice/thrice too many._

"What's worse", the Quarian continued, "a pair of YMIR mechs are guarding the security unit that Veetor is in. They still refused to listen to me".

Shepherd told Tali. "Tali, we have a sealed the door in front of us. If you can open it, we'll try to help them while there's still time".

"All right, Shepard. Give me one moment".

Shepard turned to his allies. "Get ready for a breach maneuver. Miranda and Jacob, take each side of the door. I'll be behind this barricade. Samus, can you detect the YMIR mechs past the door?".

"No. Their heat signatures are much milder than ours. However, I'm detecting the Quarians. They're pretty far to the left of the door in guarded positions firing towards the right".

"Good to know. I want you to do what you did last time and try to get around them for another flank". _Why am I asking her for another screw attack?_

"On it".

They all got into their positions and waited for Tali. Just as she'd promised, the door slid open for them. Shepard could see one of the YMIRs pounding at the Quarians, who were taking cover inside a residential unit. He zoomed in with his newly equipped sniper rifle and fired a round at its head.

His helmet's heads-up-display indicated that its shields were now gone and the armor was beginning to chip away. Both Jacob and Miranda began to fire away with their own weapons to help bring the beast of a machine down. The mech, then, turned its attention towards its newer, more aggressive opponents. By then, however, one of the Quarians had launched a missile directly at it. The blast knocked the droid to the ground. As it tried to set itself back up, the constant fire made a quick work of it. The explosion was pretty well controlled. Just as Shepherd was about to have his team move forward, a missile soared straight into the Quarians cover. He could see them all fall over, and hoped they weren't dead. Within moments, the second YMIR mech made its appearance from the far side of the cargo bay, originally unseen behind a different residential unit. With the Quarians down, it turned to face Shepard, letting loose a constant barrage of fire, forcing him and the others to keep their heads down.

"Where the hell is that stupid bitch?!", Miranda shouted over the fire, obviously referring to Samus.

And as if on cue, a great explosion was heard coming from the YMIR. Jacob stood up to look, and quickly dropped back down when he noticed the obscene amount of shrapnel flying towards him. It was no exaggeration, as the mass that once composed of the YMIR was now nothing but scrap metal. When the din died down, they all got back up to see what caused it. To nobody's surprise, they saw Samus standing there staring at Miranda with the retort.

"Look in the mirror".

 _Why can't they just tolerate each other at least for ONCE? They could hate me instead. That, or... they could fall in love with each other- No, that'd make it worse. Definitely worse._

Once abandoning his thought about his two "teammates", he concentrated his concern at the Quarians, dashing up towards the building they were in, to see if they were still alive. To his surprise, he saw Tali already there caring for them.

"They'll be fine, I think. This is your chance to talk to Veetor. Please, don't let what Prazza has done change your mind".

"You have my word, Tali", Shepard said, offering her a hand, "I wouldn't go back on that."

She took his hand and helped herself up and was headed towards a bag on the other side of the room.

"I still need to help them. I have some medi-gel in my pack. You really should go".

Shepard nodded and moved towards the security unit. Thankfully, the others were waiting for him and neither Miranda nor Samus were still arguing. When he arrived, he motioned for them to open the door, and what they found was not what they had expected.

Seated at a computer console was Veetor, talking to himself nervously.

"-Hidden, and no one can find me... not them... not anyone... can't afford to leave... must wait until it's safe... no, no, no! It will never be safe!".

Shepard approached him slowly. "Veetor. It's okay, nobody's going to hurt you".

He didn't even hear him. The Quarian was still sitting and staring and mumbling to himself.

Samus made a suggestion. "Perhaps we could shut down the computer".

"That won't be necessary". Shepherd looked at his omni-tool and fiddled with it briefly. The multiple screens began to go static. It got Veetor's attention. He realized someone was behind him. When he turned, he was relieved to see humans. "They... they didn't take you? How is that possible?".

"Take us? We've only just arrived". Miranda was a bit puzzled. "You assumed we were one of the colonists?".

"So you... you didn't see. But... I saw it. I saw everything!". He pointed to the screens as he accessed a video log.

It showed some horrendous alien creatures taking humans away. There was also a number of weird insect-like creatures scurrying around as well.

Jacob made the next observation. "This video footage is new. Perhaps we can recognize the species".

One of the monitors froze as it zoomed in on them. Miranda was the most surprised. "What the! It looks like a Collector".

"Collectors? Don't they normally keep to themselves?", Samus asked in confusion.

"Normally, but they do come out of their holes for the occasional trade, normally in slavery", Jacob corrected.

"First came the swarms", Veetor explained, "they find you... freeze you... and then the Collectors come and take you away. I analyzed them the best I could. The data is here on this omni-tool".

He offered it to Shepard, who took it without hesitation.

"Thank you, Veetor. You have some friends outside who can take you back to the Migrant Fleet".

"You mean... Tali? She did come. It is safe then". He quickly ran out to find his comrades.

Shepard, then, turned to his companions.

Miranda was displeased. "It would have been wiser to take him with us".

"For us, but not for him", Shepard replied, "we'll do well enough with this information. Let's head back to gateway station. I'm sure the Illusive Man would be interested to hear about this".

 _But, no, I lied. I wouldn't give a damn what his opinion is._


	4. Chapter 4

**Chapter III - Friendly Faces**

Once again, the chamber showing the display of the Illusive Man had not changed. There he sat, smoking another cigar, ( or was it the same one? ) casually looking over Shepard before finally responding:"Shepard, I'm glad you took the time to go to Freedom's Progress. The information we found on the Quarian's omni-tool has proven quite useful".

"Yeah, it helps to have friends that can trust you". Shepherd did not attempt to hide condescension in his remark. "I'd think it might turn your business around".

"Diplomacy is good when it works, but too much time talking can lead to inaction, something we can't afford, especially now, with the stakes so high". The Illusive Man halted for a moment as he dragged on the cigar. "Let's move on to the subject at hand. The information you obtained confirmed that the Collectors are behind these abductions".

"Confirmed? So you knew all along?". The Commander did not like being toyed with.

"I had my suspicions, but we needed proof".

"Okay, so now we know the Collectors are abducting people from your colonies. How does that involve the Reapers?".

"If you're still hesitant on this, then I see no point in trying to convince you of it. Regardless of who is controlling the Collectors, they are still abducting our people, and it's something we can't ignore".

For once, Shepard was a bit unsure of himself. If the Illusive Man couldn't prove the Reapers were involved, should he continue to help him? Entire humans from human colonies were missing, and the Council continued to ignore them. Helping humans... No, helping the galaxy was always a priority for him and he felt ashamed that he had forgotten that for a moment.

"Okay, I'll help you. How do we get the Collectors?".

The Illusive Man grinned smugly, now having Shepherd under his hat.

"The Collectors hail from beyond the Omega 4 Relay. If that doesn't ring a bell, it's a relay that no vessel has ever returned from, save for their own".

"Any idea why?".

"Nothing concrete. For the time being, my experts will continue to work on finding a way past the relay. As for you, you'll need a new team. I have constructed a list of scientists, mercenaries and specialists who would be useful for you mission. I'll be sending you their files for you to look over".

"Thanks, but I prefer my old team".

"Your old team was disbanded when you were killed. Since then, they have either dropped under the radar, or are engaged with other affairs".

"I just met up with Tali. Are you saying that was just a fluke?".

"Quite frankly, yes. Do not worry, these files of people are not members of Cerberus, and if they give any respect to anyone, it will be to you, and not me".

Shepard let out a sigh of contempt. "Very well. I suppose I'll have to take what I can get".

"Trust me, you'll be getting more than enough". Another drag. "Two more things: You'll need a ship. I just ordered one that I think will suit you nicely, and it should be docking at the station at this moment".

"And the last thing?".

"You'll need a pilot, and of this, I know you'll like him".

As if on cue, a familiar, limping man entered the holo-room from behind. Seeing him again in one piece was a pleasant sight.

"Hey, Commander. Just like old times, huh?".

"Now, Shepard", the Illusive Man said before fading away, "I leave you to your job. Make good use of your time and equipment."

With that, Shepard was finally able to pat his old friend on the back. The limping man groaned:"Hey, watch it! I've still got brittle bones".

"Sorry, Joker. I just can't believe it's you". Shepard laughed.

They were headed back out and towards the docking bay.

"Look who's talking. I saw you get spaced. I don't see anyone else rising from their grave". Joker slightly elbowed Shepard.

"Got lucky. Cerberus patched me up". They took an elevator down to the docking bay. That was when Shepherd took the time to notice Joker's uniform. "So you joined up with Cerberus?".

"Hell yes, I did. After you died, the Alliance tried to shuffle us around and pretend nothing happened, as if they could hide the fact that you were dead. They even tried to ground me. I just didn't have any other options".

"I suppose I can't blame you". Shepard nodded his head. He was beginning to wonder if Cerberus was as bad as he had remembered, or if it was faulty regeneration. "But do you think you can trust them?".

Joker stifled a chuckle. "I don't trust anyone who gets paid more than I do. But I gotta hand it to them; they saved your life, let me fly, and also, they got this...".

The elevator doors opened and they walked up to the window overlooking the docking bay. Through the window, Shepard saw another familiar, yet, special sight. The Normandy. The ship that was destroyed, had been rebuilt. With Cerberus markings declaring its allegiance, it almost looked as nice as the original, but Shepard would leave his conclusion until after his inspection of its insides. Still, it was a beautiful sight to behold. As they were staring in admiration, Samus Aran approached them.

"So this is your new ship?".

Shepherd turned to address her. "Yes, it is... Looks almost like the old one too".

"If it's all right, I'd like to have my ship moved into the hangar".

Now Joker turned to look at their new company. He began to eye the armored figure closely, half in admiration, half in caution. _Yeah, she's something, ain't she?_ It didn't stop the Commander to consult his new pilot, though. "I don't know. Joker, could her ship fit in the hangar?".

"I'd need the dimensions".

Samus ran the numbers off for him. "Ten meters, by eight meters, by three meters".

Joker nodded towards Shepard, who answered her question. "Sounds like it will. Once we've left the dock, we'll prepare for your arrival".

Samus thanked him before heading back towards her ship. Shepard watched as she left. After witnessing her in combat, he felt good knowing that she had his back.

Joker interrupted his train of thought. "Sure is beautiful, isn't she?".

"She's never taken the armor off, but through her voice, I'll bet". Shepard half joked, half be serious.

"I was referring to the ship, Commander". A sly grin streaking Joker's face as he said so.

Shepard didn't even waver at the misunderstanding, outwardly. _Shit, damn you, Joker._ He just started heading off towards their new ship. He couldn't wait to see what was inside. He was surprised when he finally boarded his new ship. Its features were slick and new, while still holding onto that tinge of familiarity. The biggest surprises were his new quarters and the ships A.I. called EDI. His quarters were furnished, like that of a luxury vessel, something that he had never had before. It was a new experience for him. As for the A.I. , as long as she was still restricted from controlling the ship, he'd be fine with her being around.

While changing into more casual clothes, he looked over the files that the Illusive Man had given him, deciding that their first stop would be Omega, the space station within the Sahrabarik System of the Omega Nebula. Several of the specialists were listed as being there, which would allow him to waste little time hiring people.

Once he had finished changing, he found himself wondering what to do next. He'd already spoken with Jacob and Miranda, whom had given their input on where to start. Miranda, being the highest ranking Cerberus officer, was made the XO of the ship, while Jacob chose a stance as the quartermaster. Both indicated they'd be busy for a while, and weren't free to speak to for long.

Among the other members of note, were Yeoman Chambers, essentially a secretary and psych evaluator, Mess Sergeant Gardner, the ship's cook, Engineers Donelly and Daniels, constantly tweaking engine performance, and finally Doctor Shakwas, who was a former member of the original Normandy. Each made mild suggestions to help upgrade the performance of the ship ( and its crew ) in some minor way. It seemed that all was well, and that he had some time to kill. Perhaps, now, he would have a chance to get some answers out of their mysterious passenger. Samus Aran had had her ship moved into the cargo hold, which was the last time he'd seen her. He decided that it was as good time.

With his mind made up, Shepard entered the lift and was headed down to the fourth deck. Once there, he navigated through the halls and passageways to reach the docked ship. The small yellow ship's lights were on, presumably because Samus was working inside. He pondered momentarily whether or not she'd notice him standing there, or if he should call her. Before having to decide, a lift lowered from her ship, revealing the armored figure. She slowly approached Shepard, and sat on a couple of crates just a few feet away from him.

That instant, she did the unexpected, for for the first time since he'd met her, Samus took off her helmet. A long, blonde ponytail dropped from underneath; and to his surprise, the warrior woman was not only strong and agile, but gorgeous as well. Even though many women he'd worked with were beautiful in their own right, he couldn't believe just how beautiful Samus was. _Goodness, is she beautiful..._ Needless to say, he was glad to see her loosening up.

"It's good to see what's behind the helmet for once", He commented. Then, he added jokingly:"For a while I was wondering if you were even human underneath".

She replied with a small chuckle herself:"Sometimes I wonder that myself as well".

Shepard decided to take a seat on a couple of crates himself. _Better to talk at the current eye level than to be above a person whom you are trying to get information from._

"Do you ever take the rest of your armor off?".

She nodded. "Back home, when things were calm, I'd almost never wear it. Still, during times of strife, I've felt really vulnerable without it".

 _Vulnerable. You?_ "Are you?".

Only a couple of questions in and he was already feeling for her. She attempted to defend herself at first, but quickly let her guard down. "Oh no! At least, not completely. I suspect I'm stronger and faster than the average humanoid, but still... the universe is a dangerous place".

"Perhaps. But there's usually a place isolated from it all that you could escape to, right? Then again, if the Reapers are returning, I doubt any settlement's safe".

"That's one thing I believe, coming from the Illusive Man".

"Did he do anything to you directly to make you think that way?". Despite his own experiences, he doubted they were in anyway similar to hers.

"Mostly his operatives, though I doubt he wasn't as involved as he claimed. They wanted to examine my DNA more closely".

"Did it have to do with my revival?". _Hmm... Curious._

Samus nodded again. "It did. I don't like talking about it, but I'd had some genetic tailoring to help me use this armor. It's why you don't see anyone else using anything like it".

"You mean... it has certain biological features that make it work?".

"You're sharper than you look, Commander", she replied, with a slight sass in her tone.

"Thanks", he responded, playing along, also finding himself subconsciously stroking his crew cut hair. "You don't have to call me that here".

"So what should I call you? Of all the people I know, you're the only one whom everyone calls by your last name. Why's that?".

"Military thing, I guess". Shepard shrugged. "But if you prefer, you can call me John".

"All right, John". Samus took a deep breath before properly answering his previous question. "Anyway, the suit is capable of bonding with me. It makes it easier to access the numerous features in it".

"Interesting". _Indeed._ Shepard was deeply enthralled with this discovery.

"But you weren't here to ask about my armor, though, were you?". _Now she's as sharp as me._

"It was an interesting topic, but no, I wasn't". Shepard leaned in to speak. "I'm more curious about whatever you did that brought me back and what effects it will have on me".

"If you're afraid of any drawbacks, don't be". She smiled slightly. It had been a long time since she'd felt so in charge when talking to a superior. "Though I doubt you'll be feeling any of these things, you might receive some enhanced reflexes, and possibly some added strength as well. However, that really depends on you. The only thing I can guarantee is that your body will heal faster than ever before, and that you'll probably live another twenty to forty good years more than the average person".

"Good to know. But why did you do it?".

She froze, just as she had done before when the Illusive Man had asked her the same question. _Bingo._ Though Shepherd didn't know, she still hadn't prepared herself to answer that kind of question, even if the summation was more than enough. "I- I need you".

 _Whoa._ Shepard's eyes widened in surprise. Samus immediately tried to correct herself. "I mean- Ugh! What I meant was that... we need you".

Then, Samus stood up, clasping her hand over her face in embarrassment. Next, she dropped it as she fixed her mistake. "You're special, Shepard. This threat of the Reapers is too great for any single person, but there's an aura about you that compels people to follow your lead. No one else in the universe could lead the Alliance to defeat them". _I'm flattered, but... uh... Uhm... Damn it._

Shepard coughed. "I appreciate all the confidence you've put into me, but certainly I'm not that special. I mean, I'm not having low self-esteem or anything, I just-". He sighed. "Look, all I wanted to say is: I'm not really one-of-a-kind kinda guy, I'm just a normal human; well, enhanced, yet still _normal_ , human".

"You may say so, but I know what I'm talking about, John. And I definitely have faith in your leadership and skills".

"I'm... glad to know it. It's... difficult to lead when your troops don't".

For a moment, it seemed as if they had nothing left to say. After two minutes of awkwardness, Samus piped up:

"A question, if I may, John?". Shepard nodded. "Do you think any others from your old crew will join you if they know you're with Cerberus?".

"I'm not with Cerberus". Shepard folded his arms. "We just have a mutual understanding. As for your question, I don't know; I would like to think they will, but it's different when the threat is not as visible as before".

"Well, I hope they do, considering what we might be up against. We'll need every hand we can get".

Shepard sighed again, but he nodded nonetheless. He had considered the possibility that a small team of specialists might not be enough. Notwithstanding, the Citadel Council would never listen to him while he had any association with Cerberus.

Slowly, he stood up and began to walk back to the bridge, muttering lowly under his breath:"I hope so too".


	5. Chapter 5

**Chapter IV - Rule of Omega**

If there was one word to describe Omega, it was "vile". Although he had been anticipating his arrival on this station for the last couple of hours, nothing could quite prepare him for it: The place emitted a vile atmosphere that would attract only those who hated people asking questions. Yet, that was one of the main reasons Commander Shepard had to set foot on this cosmos-forsaken station. He was appalled by the stench of narcotics that suddenly invaded his nostrils the moment he arrived there. The only logical response he could think of was to seal his helmet and filter it out.

Then, he heard Jacob cough several feet behind him. Miranda, who had been to Omega before, appeared immune to the fumes; while Samus was obviously unaffected while still wearing the massive powersuit. Once Jacob stopped coughing, Shepard motioned for them to move along. Before they even left the loading tunnel, they were approached by a Salarian, one who was too enthusiastic.

"Hey there, travelers! First time to Omega? It can be a bit over-"

The small Salarian was interrupted by a more massive Batarian barging past him to meet up with Shepard. He didn't even look past the little guy as he spoke directly to the Commander:"Well, Commander Shepard. So you've come here to Omega".

"You know me?", Shepard inquired, slightly annoyed that his return wasn't as secret as he'd hoped.

"Of course, I know you, human. We've had your ship tagged the moment it entered the sector", the Batarian explained, surprised, yet irritated that Shepard had returned to life, "that doesn't matter. You need to see Aria in Afterlife before you do anything here".

"Before we do anything? Is she expecting us to cause some trouble?".

"Do you really want me to answer that question?". The batarian waited for a response, but Shepard only shook his head. "Like I said. Afterlife. Now".

The Batarian walked away, grabbing the Salarian as he left, who protested all the way.

Shepard turned to his team. "Sound like a trap to you?".

"Aria is not one to kill on a whim", Miranda explained, "if anything, she'll just want to make sure that we don't make any problem for her".

"She owns the place?", Shepherd wanted to know. Miranda shook her head.

"But she might as well".

"Then I suppose we shouldn't keep her waiting".

With that, he continued down the pathway towards the rest of the station. Almost instantly, after exiting the docking bay, the night club known as Afterlife could be seen ahead, no more than a hundred yards away. Shepard wasted no time trekking up the steps past the usual line of patrons being held back by an elcor bouncer. He could hear a human arguing with the bouncer.

 _Not a good idea._

As they passed through the big doors, they found themselves in another passageway just outside the main club area. A few patrons were seated, drinking, mostly Batarians. Shepard had a natural distaste for Batarians, but did his best to avoid confrontation with them regardless. Still, his efforts remained fruitless as a small group of Batarians rose from their table and approached them. One, wearing blue, spoke for the group.

"And what are a group of humans doing here? We don't like your kind, so I suggest you leave before things get ugly".

Shepard played it cool despite the obvious trigger-happy attitude of the Batarian yahoos. "If things do get ugly, it's not me that's going to regret it. Certainly you can tell we're not your average human rabble".

He gave the pistol at his side a rub with his index finger, just for good measure. The Batarian took a look, and realized that he and his comrades were outmatched. Without even a proper retort, they were headed back to their seats. Shepard took his cue to walk away before they changed their mind. Behind him, he could hear Samus complimenting him.

"I'm impressed, Shepard. That was really nice of you to let them live".

 _Oh but if I and they were elsewhere, I don't think so._

Shepard grinned. "I'm just not in the mood right now for trouble. If possible, I'd just like to hire these specialists and get out with no conflicts whatsoever".

"If only things were that easy", Jacob remarked.

The next door led into the main club. Asari dancers could be seen above the bar moving to the pulsing rhythm of the music throbbing through the ears of everyone who was in Afterlife. The place was full of life as people were laughing, dancing, and shouting all over the place. Shepard noticed the elevated platform on the other side of the bar, and proceeded to head over there, assuming that it was where their mysterious host was.

The four humans approached the platform, and the figure could more easily be seen. It was an Asari, as expected, whom although was not facing them, giving off an aura of an executive business woman. Just before he reached her, they were halted by her security chief, another Batarian. He also heard the Asari speak firmly against him coming closer.

"Stay where you are, Shepard, and I'll decide whether or not you're allowed on my station".

The Batarian began to scan the commander and his companions. The others were told to stay further away while negotiations would be made with Shepard. Shortly after, the Batarian finished his scans.

"It's him, alright".

That was when the Asari turned to face the Commander. She had a couple of facial tattoos that supported her determined, business-only appearance, and reminded Shepard to at least be polite enough not to piss her off.

"I was told you wanted to see me".

The Asari sat down on the luxurious couch at the edge of the platform, facing the Commander. She motioned for him to sit as well, which he did so, but at a relative distance. Then, she finally spoke up:

"Let's just say that when word is passed that the Hero of the Citadel might be alive, and just so happens to show at my station, I get curious. You're not here to just relax and 'shoot the breeze' like the others. You're here looking for something. I believe the best way to ensure that you don't go asking the wrong people and causing messes is to talk directly to me".

"So you do own Omega".

She chuckled at the statement before standing up and turning back to the station beyond the platform, with the dramatic rise of her hands, she declared:"I am Omega".

Aria turned back to Shepard and stepped towards him, placing one of her high-heel booted feet uncomfortably close to him.

"And I like to keep it that way. I just want to make sure that you know the rule around here before you go blasting your way around".

"And that rule is?". Shepard raised an eyebrow, not intimidated by her proximity.

Aria sat back down in a relaxed pose and raised a single finger. "Don't fuck - with Aria".

Shepherd held back a chuckle, but nodded his head in acknowledgement. "All right, Aria. I'll keep my distance, but I expect the same from your goons".

"Then we are in agreement". She smiled smugly as she took a sip from a drink she had next to her. "So, what exactly are you looking for?".

"Specialists. I'm recruiting for a hazard op, and I need some elite personnels. Non-military personnels".

"I'm sure you can find plenty of scums willing enough to sign up for your suicide run if you raise the price high enough".

"Not what I'm looking for. I already have files on the two I'm looking for. I need Dr. Mordin Solus and the mercenary Archangel".

"Those two? Well, I might be able to help you with Dr. Solus, but Archangel is being a bit elusive at the moment".

"And why is that?", Shepherd pondered aloud.

Aria couldn't help but let her smile widen as she explained. "Because he's pissed off every major mercenary group here. I expect he'll be laying low for a while. Perhaps if I catch wind of him, I'll let you know".

"That'd be appreciated. What about the good doctor?".

"He's got a clinic in the Gozu District. Of course, those slums have been quarantined since the plague began".

"There's a plague in the slums? Is Mordin trying to suppress it?".

"From what I've gathered, he's close to making a cure. If you wait a while, you might be able to see him".

"We can't afford the wait. If my team got in hazard suits, would you allows us to go in? We'd be quick to assist him in finishing the cure".

"And I suppose you have medical staff suited to do so?", Aria sarcastically asked. She shook her head briefly. "Whatever, humans are immune to the virus. I'll let go if you must, but you won't come back in until that plague is gone. Are you in that much of a hurry?".

Shepard nodded solemnly. The Asari sighed in response.

"Very well. Tell the guard at the slum entrance I've given you permission to pass".

Shepard stood up, and with a mild bow of respect, thanked her for her assistance. He, then, returned to his crew. They walked briskly out of the club while Shepard told them about their destination. The others agreed to his plan of action, and were quick to follow. Still, the situation in the slums was curious. It was left for Jacob to pop the question in everyone's mind.

"Why do you suppose the virus doesn't affect humans?".

"Humans do have a varied immune system", Samus conjectured, "some things that effect other species greatly don't effect us at all, and vice versa. It's also possible that a human designed it".

"And release it in the Gozu District?", Miranda inquired, "what would they gain by doing that? It makes little sense for some sophisticated human scientist to release a plague there".

"Unless they were to test the effects of it", Samus countered.

It detracted Miranda slightly to hear the armored figure still attempt to disprove all of her hypotheses, but Samus didn't seem to be too interested this time. Miranda considered to continue to defend herself, but eventually decided against it. Within several minutes, the squad reached the door to the Gozu District. A Turian guard was holding off a human woman from entering. They were arguing back and forth for awhile by the looks of it.

"Sure", the guard spat, "of course you just want to get your stuff, and probably the stuff of a dozen other dead citizens. Probably caused it too, didn't you?".

"Asshole!", the woman rebuked, "why the hell would I do something as stupid as this? I've got friends who aren't human, you know. Besides, the Vorcha are immune too. Why don't you talk to them about the virus?".

"Because they're on the inside, and I'm staying on the outside".

Shepard politely stepped between the two. "I understand that the situation is pretty dire, but Aria just told me that my team can go through".

"You spoke to Aria?". The guard was rather impressed, but not quite convinced. "And what did she expect you to do?".

"Nothing, really. What we plan to do is another. We're here for Mordin Solus. As soon as he creates a cure, we'll be on our way out with him".

"That crazy doctor? Hell, I'd be glad to see him go. But if you go in there, I'm not letting you back in until I'm told to open the place up".

"That's fine with us".

The guard, next, stepped aside for Shepard and his team. The woman tried to go in with them, but the guard stopped her again.

"Oh, so they can go in but I can't. Oh! I forgot to tell you that Aria said I could go back in too!".

"Yeah, right. Whatever".

And Samus thought that the main part of Omega looked and smelled awful. The slums were another story entirely. Miranda was able to sum it all up in a single word: Pisshole. She couldn't help but agree with her. There was nothing appealing about this place. How a Salarian doctor could set up a clinic here was... Well it made perfect sense, but how someone was capable of pulling it off was different. Samus couldn't help but admire the amount of dedication it must have taken for Dr. Solus to take on such a task.

Immediately after being allowed past the border guards, there were signs of riots. Trails of blood, dead bodies and burned-out electronic panels to people's homes. the place really went to hell since the plague had begun. Shepard still took the precaution of wearing his helmet, as did the Cerberus agents, just in case an alteration to the disease had been made to affect humans.

After turning down a hallway, they spotted several Blue Sun mercenaries coming out of an apartment unit with their new trove of stolen goods. One of them, a Batarian, noticed the newcomers and instantly began to pull his pistol. Samus halted him in his tracks with a cold blast from her ice beam. The others, now alert to the intruders, dove for cover and began to fire back. Commander Shepard and Miranda ducked around some nearby crates while Jacob hit the dirt in a prone position. Samus took the opportunity to finish the frozen thug with a missile before finding a pillar to hide behind.

The confrontation didn't last too long, as the other Batarians of the Blue Suns were sick, and not fully competent, while the humans were simply competent. A few barrages of fire from Shepard's assault rifle and Miranda's submachine gun kept their heads down while Jacob and Samus got close enough to finish them off quickly. As they reformed, Samus noticed a bystander. A sickly Batarian who was probably the victim to the Blue Suns robbery. She pointed him out to Shepard, who decided to approach him. The Batarian didn't seem to have any trust in human kindness. It raised a pistol with weakened fingers at them.

"Keep away, humans! I know...". He coughed. "... what counts as 'hospitality' amongst your kind".

Shepard wasn't afraid of him firing, but he didn't want to alarm him when it wasn't necessary, so he holstered his weapon as he spoke. "You look injured. Do you need any assistance?".

"No...". He coughed again. "... no injury. Just this damn plague. Why should you care? Your kind...". Another cough. "... caused it".

"I'm not a resident here. I'm looking for Mordin Sol-".

"I said keep away from me! Don't think that I... that I...". Cough after cough. The Batarian lowered his arm as it fought the disease that was slowly killing him. Shepard made no hesitation as he knelt down and applied a medi-gel to him.

"Hey! Stay with me!".

As the medi-gel kicked in, the Batarian found himself strong enough to stand.

"You... saved me?", he asked weakly.

"I'm not here to kill. I'm here to help. That medi-gel won't cure you, but it should relieve some of the symptoms, for now. I need to find Dr. Mordin Solus's clinic. Do you know where it is?".

"Yes. It's farther down this hallway and across the Azu Bridge. But I wouldn't trust that doctor if I were you".

"And why is that?".

"Because he's ruthless". The batarian sounded slightly scared. "I saw a group of Blue Sun mercs try to shake him down for protection. He had them all shot".

"Even still, he's developing a cure. If I get there, I'll have someone come and get you". Shepherd turned and began to leave, but was halted shortly after.

"Wait, human. I... I should thank you".

"It's okay". Shepard nodded and he carried on his way.

Seeing Shepard continue to diffuse sticky situations with mere words amazed Samus. As good as she was at analyzing people and cultures, she still couldn't get a bead on how he was able to do it. Was it the military training, his spacer upbringing, or did it just come naturally to him? Despite her seeming ineptitude, she was glad that she had picked the right man to follow.

Samus took the point as they passed the Azu Bridge, hoping to detect some new targets to give her a new focus instead of her thoughts about Shepard. This was to no affect. After turning around another corridor of halls, the team discovered a pair of YMIR mechs guarding a door with a man behind a shatter-proof window monitoring them. Shepard approached them calmly, noting the sign above indicating that it was the clinic.

The man eyed them wearily, but seeing that they weren't wearing any mercenary insignia, he waved them through with a warning. "Keep your weapons holstered and cause no problems, or else we'll have a problem".

Shepherd nodded politely as he walked past the now opened doors. Knowing that she couldn't 'holster' her cannon, Samus just kept her arm at her side as she sauntered in behind him. The clinic was full of patients. A number of nurses tried to help those who were ailing the most, while the others waited by. Coughing was the most common sound to be heard. Samus couldn't help but stare at the copious amounts of people, feeling pity for those who'd had to go through what she could only imagine was a painful experience.

Shepard, however, was a little more preoccupied looking for Mordin Solus. He followed a few passageways until he thought he could hear the sound of the Salarian giving out a prescription. As he turned the last corner and entered the closest room, he saw him. The description in the codex Samus had was too generous, showing off his picture from a time when he must have been a younger, keener medical officer. The Salarian bent over a mix of chemicals was far older. The wrinkles of time shown on his face quite clearly, even from the eschewed perspective. Yet, despite the age, the hands of the doctor were fast and unwavering, moving as if by instinct rather than thought.

"Professor Mordin Solus?", Shepard called to him respectively.

The doctor turned from his work, hearing the unfamiliar voice calling his name. He took a second to study the man asking him before beginning a nonstop barrage of questions which he'd answer himself.

"Armed soldiers. Quarantine still in effect, yet not wearing mercenary uniform, yet clearly outsiders...".

With this rant, Samus was able to realize that he most certainly was a creature of thought and not instinct. He simply thought faster than the average human. Not to mention out loud as well. As interesting as this was, she felt a need to put a stop to it.

"Professor, you can calm down. We're here to ask for your help... outside the current viral outbreak".

"Oh?". The professor eyed them again. "Freelance soldiers working for great corporation?".

"Ever heard of a group called Cerberus?", Samus spoke even before Shepard or Miranda could say anything, ensuring that he knew who exactly they worked for.

Mordin was well informed. "Quite. Heard they only worked with humans. Branching out, it seems? Must be something important, if so".

"It is". Shepherd finally got a word in, eyeing Samus and letting her know that he would take it from there. _Thank you very much._ "The Collectors have been abducting people from entire human colonies, using technology and bioweapons that we've never seen before. You were at the top of the list of specialists who would be more than qualified to assist".

"Hmm... Collectors. Our goals may be similar. Virus created by an unknown assailant. Collectors perhaps the only race with technology to develop it". He put a three digit hand to his chin as he pondered the thought, but he quickly stopped as he remembered his current objective. "Discussion will have to wait. Have cure to virus now. Need to get it to the ventilation systems blocked by Vorcha".

He turned his head to the Commander before finally saying:"Need to kill them".

Shepard took a step forward, ready to speak again, but then a noticeable fluxuation in the room's lights halted him. The air also became slightly more stale, something he never thought he would have been able to pick up before. Mordin consulted his omni-tool before recognizing the problem. "Ventilation has shut down. Vorcha trying to prevent cure. Need to stop them now".

Mordin started moving hectically around his office, gathering supplies and the like. Shepard took this as an opportunity to stand in his way, getting his full attention. "Give me the cure. My team and I will go ahead and take care of the Vorcha. Your job is here with your patients".

Mordin nodded, adhering to his advice. "Very well. I'll stay back with them".

 _Finally._

"Good". Shepard started out before he remembered something. "Oh, I also met a Batarian near the entrance of the district. He's too sick to make it here on his own".

"I'll have one of my machines sent to escort him. Similar note, my assistant, Daniel, went into Vorcha territory looking for Batarians. Hasn't come back for a while. If possible, keep an eye out for him".

"Will do". Shepard nodded, turning around and making his way out of the office with his team. "Let's go, team, we've got a plague to fight, figuratively".

 **Note: Alright everyone, this is the last chapter I edit from** **Knight on Bald Mountain. After this, I'll write it with my own ideas; also, the story on Knight on Bald Mountain's page will be deleted and you won't have to be confused because there are two Mass Effect: Factor X stories. Thank you for reading and reviewing this story, I appreciate it. :D**


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